The Doctor and the Cave
by happybluemo
Summary: When the Doctor, Amy, and Rory discover that Cave Johnson is still alive, they have no choice but to investigate and become a vital participant in the war against the Combine by providing Gordon Freeman with the equipment he needs. Alternate universe, some elements of the canon universe.


"Here we are!" exclaimed the Doctor as he stepped out of the TARDIS onto a white-paneled floor.

"Um, Doctor... Where are we?" asked Amy. Rory followed closely behind her.

The Doctor immediately licked his right index finger and stuck it up in the air. "A laboratory, as it seems."

Rory wasn't quite satisfied with his answer. "A laboratory where, exactly? And when?"

"Now that I'm not sure… I'd say somewhere in the United States, around…" the Doctor approached a white-paneled wall and felt it. "Somewhere in the 2000's. Not sure exactly when."

"Maybe we could ask someone?" offered Amy.

"Good idea, except where _is_ everyone?" the Doctor trailed off dramatically as he took in his surroundings. The walls and floor were both made up of white panels. Some of them were stained or written on with some sort of brownish black substance not unlike dried out blood. The ceiling was made up of a brown tiling. One of the three walls of the room had a doorway with a sort of force field within it, leading to another room. This wall had the same brown tiling as the ceiling. Opposite this wall was a round, padded lift with no buttons. "Well let's explore, shall we?"

The Doctor straightened his bow tie before analyzing the force field in the doorway. "Now what is _this?_" he said to nobody in particular. He was fairly impressed. "Now this isn't supposed to be here for at least another 50 years..."

"So what is it, then?" asked Amy.

The Doctor took out his sonic screwdriver and scanned the force field. "Some sort of vaporization field. But it only vaporizes certain things, like… I don't know, a box? Allow me to demonstrate." The Doctor walked over to a security camera that was once on the wall, but now lay dormant on the floor. He kicked it into the vaporization field. The camera took a few moments to break up into billions of black specks before the specks fell to the floor and vanished. The Doctor then proceeded to walk through it himself. Although he felt a sort of tingling sensation, death did not follow. "See? Fine."

Rory and Amy both reluctantly followed the Doctor into the next room. In the middle of the room was a fairly large red button with a fairly large grey box on it. A dotted blue line on the floor made its way to a black X next to a round door on the left wall. Amy picked up the box, tossing it in her hands. When she replaced it back on the button, the dotted line turned orange, the X into a checkmark, and the door opened. Behind the door was another vaporization field, and behind that another lift.

All three of them made their way to the lift. Both doors closed automatically behind them, and the lift made its way upward. "So I suppose the purpose is to solve puzzles, isn't it? I love puzzles!" Exclaimed the Doctor.

"Okay, but where are all the people?" asked Amy.

"Well that's what we're going to find out, isn't it?" answered the Doctor.

The lift stopped abruptly, opening its doors to a hallway similar to the one they began with. The differences were that the ceiling was also the white paneling, and there was a large monitor mounted to the wall with a rather large number "4" on it in black. The hallway zigged a little, turning left then right before it led to the actual room.

Before the three could make their way to the room, they were met with a slightly disheveled looking woman with the top part of her orange jumpsuit tied around her waist, and her white tank-top showing. She wore a long ponytail in her black hair, and rather strange looking metal springs attached to her knees forced her to walk on her toes. In her heavily bandaged hands was an odd white device not unlike a large and sleek gun. She looked extremely surprised to see the Doctor and his companions. She hastily put down the device and started quickly speaking in sign language- one of the only languages the TARDIS couldn't automatically translate. Luckily the Doctor "spoke" everything, and he could easily understand what she was saying.

"I suppose so," said the Doctor, seemingly answering a question that the lady had signed to him. "Might I examine that device?"

The woman complied. The Doctor bent over and picked it up, analyzing every angle before breaking out his sonic and scanning it.

"Now _that _is cool! A bit too early, though…"

Amy was curious now. "What is it, Doctor?"

"Quantum tunneling! It uses a miniature black hole to make two holes in the fabric of space, and then bends it to bring the two together. Portals, if you will."

"So in one, out the other?" confirmed Amy. This time it was the nameless woman who nodded her head. She then signed something to the Doctor.

"Oh, sure! Please do!" answered the Doctor, handing the quantum tunneling device to the woman. She put her right hand underneath a small bit of casing and wrapped it around a small handle within. Her left hand supported the "barrel" of the device.

The woman pointed the device at a wall and fired. A small blue stream of light made its way to the wall and opened up a large blue oval shape, with something around the edges not unlike blue fire. She then proceeded to aim and fire at another wall, this time opening up an orange one. Instantly the portals connected. They could all see through the blue portal what they would see if they were standing right where the orange one was, and vice versa.

"_Wow_ that is cool," remarked Amy as she stuck her hand through the blue portal and watched it come out the other.

The Doctor stepped entirely through the blue portal- and came entirely out the orange one. "I love that!" He then walked up to the nameless woman. "So I do have a few questions though. Where are we, what's your name, and who runs this place?"

The woman took great care explaining everything so the Doctor could understand.

"C-Cave? Cave _Johnson?_" The Doctor ran his fingers through his hair as he paced back and forth. Was this even possible?

"What's so special about this Cave Johnson guy?" asked Amy.

"I just… maybe I'm thinking of someone else. But just in case…" the Doctor paused as he walked back to the woman, who was at least a good 5 inches shorter than him. "Chell… let's go meet your boss. If she is what you think she is, then we should have very little trouble." The Doctor held up his sonic screwdriver. "Now let's go."

The Doctor cautiously stepped out of the TARDIS, with Chell, Amy, and Rory following behind him. They were in a large cylindrical chamber with some sort of enormous mechanism dangling precariously from the ceiling. Wires and cables were strung up connecting it to various other parts of the room, and a small staircase led to a catwalk surrounding it. It strongly resembled a woman tangled in wires hanging from the ceiling. Something at the bottom strongly resembled a head with a single orange eye. This head turned to face Chell and spoke with a soothing, robotic voice.

"So you found me. Congratulations."

It was the Doctor, of course, who replied to it.

"Yes, we found you. But the thing is, I'm not sure what I'm talking about when I say 'you.' What are you? What is your name?"

It just laughed. "Do you really think I'd just tell a stranger? How about I ask who _you_ are?" It paused. "And how you escaped?"

The Doctor knew what it meant by that, but nobody else did. Clearly this AI knew more than the Doctor thought.

"Doctor, what does it mean by that? Escaped from what?" asked Amy.

"From the time war. But how does it know about that?" The Doctor walked toward it and excitedly leapt up the steps and onto the catwalk.

"You still haven't answered my question," reminded the computer.

The Doctor looked her straight in the "eye" as he spoke. "I am the Doctor. I am the last Time Lord, but maybe not. And I'm looking for Cave Johnson. Who are you?"

The AI hesitated before it answered. "GLaDOS. Genetic Life-form and Disc Operating System. I run this facility. If you're looking for Cave Johnson, you missed him by about 30 years."

"Why? What happened?" the Doctor persisted.

GLaDOS chuckled. "Now that you'll have to find out for yourself, Doctor."

The Doctor pulled out his sonic screwdriver and sonic'd GLaDOS, analyzing the results.

"What is that?!" exclaimed GLaDOS.

The Doctor didn't hesitate to answer with a grin, "Now that you'll have to find out for yourself, GLaDOS." He then turned around and hurried back to the TARDIS, rushing everyone in and hastily working the controls.

"So what _did_ happen to Cave Johnson, anyway?" asked Amy.

"In 1979, he died of lunar sediment poisoning. At least, that was the cover story. But someone wanted him gone. By that time he had gotten very sick from the poison, so his mind was all wonky. He kept doing stupid stuff, getting in trouble, putting the scientists in danger. Around that time, they were working on something called the Portal Project. In the first few tests with these portals, there was some accidental time travel involved. Completely unintentional, and they did end up fixing it.

"However, that gave Cave Johnson an idea. If he were to "discover" time travel, he would be one rich man. He didn't care that it was hundreds of years too soon. He already knew how to travel through time, of course. He used power from his TARDIS to make his own time travel machine. He didn't want to share the TARDIS itself, of course, that was Time Lord technology. He had to make it something else, like-"

Chell answered his sentence with her hands.

"Exactly. How did you know?"

Chell answered as part of the control panel exploded and the TARDIS shook.

"Ah. Forgot about that."

"So Cave Johnson is a Time Lord?" asked Rory.

"Yes, exactly. He escaped the time war and hid in the best place he could find; an abandoned salt mine 4 kilometers underground," the Doctor clarified, "That's what the laboratory is built out of. It's an old salt mine somewhere in Ohio."

"What actually happened to him, though?" Rory asked.

"The boat they were working on. The time traveling one. The cover story was that Cave died from lunar sediment poisoning in 1979. But that's not what happened. The scientists had an idea. There was a test run planned for some time in 1979, they were going to see if the boat worked. The scientists made sure that Cave Johnson was on that boat when they did the test, and made sure something was done wrong. Basically, they cast him off somewhere in time and space and left him there. They didn't know, of course, that he was a Time Lord, that he had a TARDIS, all that stuff.

"But his assistant did. His assistant knew what he was. It was her consciousness that was put into GLaDOS, that's why GLaDOS knows. And then, as any reasonable person would from being unwillingly shoved into a computer, she went mad and flooded the whole facility with neurotoxin, killing all the scientists but one. And you know who that one is?" the Doctor turned and pointed to Chell. "Your adoptive father. But that part isn't really relevant, I just thought you ought to know. He saved your life a few times, too."

"So where are we going, and how do you know Cave Johnson?" asked Amy.

"He was a friend of a very distant relative. He never learned to speak, read, or even write in Gallifreyan, he was too young when the time war ended. Not too young to not escape though, apparently. We are going to 1979, the year Cave Johnson 'disappeared.' We are going to witness the first test run of the Aurora Borealis!" the Doctor exclaimed excitedly.


End file.
